             [clojure.java.io :as io]
             [me.raynes.fs :as fs]
             [clj-bwa.core :as bwa])
-  (:import [clj_bwa.jna MemOption FastmapOption]))
+  (:import [clj_bwa.jna AlnOption SamseOption SampeOption SwOption MemOption
+                        FastmapOption]))
 
 (defmacro with-out-file
   [f & body]


;; samse test
;; ----------

(with-state-changes [(before :facts (do (prepare-cache!)
                                        (doseq [f test-db-files]

;; bwasw test
;; ----------

(fact "about sw-option"
  (type (bwa/sw-option)) => SwOption
  (type (bwa/sw-option nil)) => SwOption
  (type (bwa/sw-option {})) => SwOption
  (type (bwa/sw-option {:skip-sw 1})) => SwOption)

(with-state-changes [(before :facts (do (prepare-cache!)
                                        (doseq [f test-db-files]
                                          (fs/copy f (str temp-dir "/" (fs/base-name f))))
